Statistics: Genome Annotation

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Rattus norvegicus Genome: Statistics -- Build 2 Version 1

Summary of the GenBank source sequences, the contigs, and the features annotated on the sequence based on genomic sequence information available on Jul 22, 2003. Also summarizes the objects on each non-sequence-based map in the MapViewer.

These statistics are based on the assembly and annotation process documented here.

Resource	Scope
Cytogenetics	A cytogenetic resource of FISH-mapped, sequence-tagged clones
dbSNP	Database of SNPs and other genetic variation
LocusLink	Focal point for genes and associated information (fruit fly, human, mouse, rat, zebrafish)
RefSeq	NCBI Reference mRNAs and proteins for human, mouse, rat
UniGene	Human UniGene clusters
UniSTS	STS markers

GenBank Source Sequences

Sequence type	Number used	Length	Total
HTG Phase 1
HTG Phase 2
HTG Phase 3	152	2.68976x10⁷
WGS	137840	2.56627x10⁹	2.59317x10⁹

Framework Assemblies

Number of contigs generated	841
Length of sequence assembled	2,839,480,000

Contigs categorized by type of source sequence

Type of source sequence	Number used	Length (bp)
Draft only	740	2,813,750,000
Finished only	101	25,726,700
Draft and Finished	0	0

Contigs categorized by size

Range (kb)	Number	Length (bp)	% total
< 300	462	54,052,000	1.9
300 – 1000	109	56,537,200	1.99
1000 – 5000	123	309,847,000	10.91
> 5000	147	2,419,040,000	85.19

N50 Contig Length (Kb)

Reference	All	-
Reference	Mapped	19,234
NCBI_NT	All	-
NCBI_NT	Mapped	235

Genes, Exons and Introns

Statistic	Evidence	count	min	max	avg
*Assembly: Reference*
Exons	EST	5,793	9	11,864	225.43
	Predicted	76,438	4	11,558	228.6
	mRNA	108,990	2	10,024	212.67
Introns	EST	4,890	58	483,898	4,691.02
	Predicted	64,206	51	471,438	4,598.33
	mRNA	87,826	2	484,231	4,496.32
Transcripts	EST	455	476	1,631,482	60,911.7
	Predicted	12,232	269	731,644	25,559
	mRNA	11,334	196	1,531,854	42,234.9
Transcripts per Gene	EST	-	1	1	1
	Predicted	-	1	1	1
	mRNA	-	1	3	1
One-exon Genes	EST	12	-	-	-
	Predicted	3,000	-	-	-
	mRNA	716	-	-	-
One-exon Transcript	EST	12	-	-	-
	Predicted	3,000	-	-	-
	mRNA	716	-	-	-
Exons per Gene	EST	-	1	87	12
	Predicted	-	1	161	6
	mRNA	-	1	140	9
Exons per Transcript	EST	-	1	87	12
	Predicted	-	1	161	6
	mRNA	-	1	140	9

Object count: Clones, markers, genes, variation annotated on the sequence

Chrm	BES	Comp	Contig	CpG	Genes_seq	Hs Ests	HsUniG	Mm Ests	MmUniG	Model	Pheno	RNA	Rn Ests	RnUniG	SAGE tag	STS	Variation
*Assembly: Reference* Mapped (Not placed)
1	14,003 (286)	12,098 (416)	27 (25)	29,671 (418)	2,890 (43)	186,488 (449)	4,487 (52)	56,693 (99)	2,696 (16)	4,943 (95)	23	2,663 (36)	55,566 (262)	9,382 (74)	11,034 (72)	2,602 (17)	2,814 (16)
2	13,571 (224)	11,934 (376)	19 (17)	22,105 (475)	1,567 (37)	98,923 (943)	2,932 (60)	27,772 (316)	1,472 (28)	3,145 (85)	18	1,368 (34)	28,445 (393)	5,665 (92)	6,375 (97)	1,688 (29)	1,720 (35)
3	9,169 (83)	7,885 (190)	17 (15)	19,554 (214)	1,639 (18)	156,622 (540)	3,056 (25)	35,940 (129)	1,735 (14)	2,927 (33)	12	1,513 (13)	34,441 (91)	5,961 (28)	7,118 (27)	1,618 (7)	1,706 (6)
4	9,934 (101)	8,256 (236)	15 (11)	18,240 (212)	844 (12)	87,085 (3,194)	2,514 (34)	24,495 (416)	1,299 (15)	814 (12)	13	837 (12)	26,400 (265)	5,111 (45)	5,841 (44)	1,516 (10)	1,471 (10)
5	8,936 (142)	8,324 (269)	24 (20)	19,419 (231)	1,383 (12)	116,210 (255)	2,658 (19)	27,125 (55)	1,442 (9)	2,557 (36)	-	1,263 (10)	27,975 (123)	5,284 (38)	5,827 (27)	1,506 (9)	1,490 (11)
6	7,601 (76)	6,846 (196)	10 (10)	15,126 (201)	1,035 (15)	82,955 (1,299)	2,067 (29)	18,917 (302)	1,043 (12)	2,030 (30)	-	911 (15)	19,998 (429)	4,040 (55)	4,429 (76)	1,119 (8)	1,063 (19)
7	7,536 (57)	6,821 (145)	13 (11)	18,556 (167)	1,392 (16)	114,348 (86)	2,309 (15)	32,982 (10)	1,356 (5)	2,489 (35)	-	1,281 (16)	31,999 (115)	4,974 (25)	5,946 (18)	1,304 (3)	1,604 (12)
8	6,922 (40)	5,737 (102)	8 (8)	15,477 (108)	1,190 (10)	86,747 (847)	2,155 (18)	31,250 (99)	1,182 (10)	2,129 (15)	-	1,109 (10)	25,342 (216)	4,674 (28)	5,352 (51)	1,311 (6)	1,214 (7)
9	6,218 (46)	5,230 (128)	8 (8)	12,985 (132)	809 (7)	56,334 (709)	1,492 (17)	16,684 (12)	798 (7)	1,633 (31)	-	748 (6)	17,171 (45)	3,263 (10)	3,571 (9)	885 (5)	888 (6)
10	5,527 (45)	5,092 (105)	15 (8)	17,912 (68)	1,586 (12)	151,365 (38)	2,953 (7)	50,121 (6)	1,935 (3)	2,462 (20)	26	1,523 (10)	40,581 (42)	6,183 (10)	7,799 (9)	1,619 (4)	1,932 (2)
11	4,921 (64)	3,810 (106)	6 (5)	8,855 (106)	600 (14)	40,949 (516)	1,200 (13)	8,954 (154)	575 (8)	1,123 (22)	1	528 (12)	11,636 (367)	2,334 (38)	2,590 (44)	638 (7)	663 (6)
12	2,277 (37)	2,590 (90)	14 (11)	12,111 (155)	592 (15)	53,077 (452)	983 (10)	15,436 (53)	603 (5)	1,091 (23)	7	565 (11)	13,845 (116)	2,463 (31)	2,699 (26)	651 (1)	766 (8)
13	5,555 (21)	5,214 (72)	15 (13)	11,705 (92)	686 (6)	42,547 (303)	1,393 (8)	10,984 (71)	660 (3)	1,295 (13)	5	608 (5)	14,040 (39)	2,705 (13)	3,000 (8)	919 (5)	703 (3)
14	5,939 (105)	5,116 (205)	14 (12)	12,412 (228)	745 (18)	53,091 (110)	1,398 (14)	17,294 (11)	770 (4)	1,466 (43)	7	673 (14)	15,408 (54)	2,916 (14)	3,117 (11)	820 (1)	825 (3)
15	6,431 (135)	5,172 (168)	14 (11)	11,061 (220)	862 (27)	52,769 (408)	1,255 (13)	11,772 (137)	635 (3)	1,611 (49)	3	792 (23)	13,199 (97)	2,660 (34)	2,825 (19)	790 (7)	666 (4)
16	4,866 (118)	4,525 (150)	9 (8)	10,434 (172)	661 (30)	36,855 (3,565)	1,122 (40)	9,783 (440)	555 (23)	1,336 (44)	4	574 (29)	12,993 (508)	2,461 (52)	2,781 (90)	709 (10)	675 (17)
17	4,910 (34)	4,801 (80)	12 (8)	12,460 (50)	700 (6)	53,382 (11)	1,289 (5)	10,954 (4)	656 (2)	1,583 (14)	4	631 (5)	15,587 (17)	2,685 (3)	2,868 (2)	788 (1)	755 (1)
18	4,564 (23)	3,940 (76)	13 (12)	9,758 (99)	563 (4)	53,501 (182)	1,164 (8)	10,127 (6)	638 (4)	1,239 (7)	6	511 (3)	11,540 (21)	2,348 (6)	2,523 (7)	704 (1)	550
19	2,974 (47)	2,806 (116)	7 (6)	9,537 (157)	608 (7)	39,232 (86)	1,027 (12)	11,092 (12)	612 (3)	1,127 (19)	6	569 (7)	12,896 (93)	2,384 (22)	2,651 (17)	605 (2)	623 (2)
20	2,651 (16)	2,919 (68)	10 (9)	10,661 (131)	553 (11)	44,570 (1,130)	983 (10)	8,444 (49)	466 (15)	1,059 (22)	5	516 (11)	12,486 (116)	2,046 (32)	2,394 (31)	503 (7)	834 (20)
X	7,773 (94)	8,694 (273)	21 (18)	7,491 (111)	1,075 (7)	103,246 (763)	1,951 (11)	22,550 (15)	915 (4)	1,551 (20)	-	899 (7)	12,627 (84)	2,382 (10)	2,732 (24)	767 (4)	466
Un	(7,459)	(6,532)	(203)	(6,644)	(740)	(14,692)	(420)	(6,605)	(179)	(1,823)	-	(549)	(5,705)	(802)	-	(152)	(285)
*Total*	142,278 (9,253)	127,810 (10,099)	291 (449)	305,530 (10,391)	21,980 (1,067)	1,710,296 (30,578)	40,388 (840)	459,369 (9,001)	22,043 (372)	39,610 (2,491)	140	20,082 (838)	454,175 (9,198)	81,921 (1,462)	93,472 (709)	23,062 (296)	23,428 (473)

Chrm	BES	Comp	Contig	CpG	Genes_seq	Hs Ests	HsUniG	Mm Ests	MmUniG	Model	Pheno	RNA	Rn Ests	RnUniG	SAGE tag	STS	Variation
*Assembly: NCBI_NT* Mapped (Not placed)
1	566 (20)	23 (1)	20 (1)	661 (72)	90 (2)	4,248 (500)	117 (11)	1,168 (38)	76 (4)	123 (2)	-	85 (2)	1,881 (145)	280 (18)	-	69 (5)	79 (11)
2	1,035 (24)	20 (1)	16 (1)	207 (11)	16	506 (1)	31 (1)	223	14	26 (2)	-	11	300 (1)	53 (1)	-	19 (1)	15
3	(86)	(3)	(2)	(143)	(19)	(3,082)	(34)	(1,053)	(27)	(26)	-	(17)	(528)	(82)	-	(18)	(32)
4	513 (138)	23 (4)	10 (3)	336 (71)	22 (2)	1,103 (91)	70 (5)	329 (7)	38 (3)	22 (2)	-	22 (2)	447 (58)	110 (13)	-	34 (4)	25 (8)
5	(27)	(1)	(1)	(10)	(3)	(362)	(4)	(111)	(2)	(4)	-	(2)	(42)	(8)	-	(2)	-
6	53	1	1	25	6	499	10	218	9	6	-	5	173	19	-	7	8
7	208	6	5	185	15	558	36	122	19	27	-	13	152	48	-	6	10
9	125 (35)	2 (1)	1 (1)	48 (23)	5 (3)	1,937 (173)	13 (8)	8 (131)	4 (3)	6 (4)	-	3 (3)	56 (67)	14 (14)	-	2 (6)	7 (1)
10	84	2	2	95	17	1,429	17	175	11	21	-	17	1,181	41	-	12	30
12	156	11	3	391	38	2,509	66	1,847	46	43	-	37	863	132	-	42	45
13	135 (18)	3 (1)	3 (1)	31 (30)	5	125	8	40	6	6 (1)	-	4	44 (4)	16 (2)	-	2 (2)	4
14	(61)	(3)	(3)	(132)	(9)	(580)	(23)	(150)	(16)	(18)	-	(8)	(179)	(46)	-	(10)	(9)
18	237	7	6	131	6	372	30	33	12	18	-	6	154	30	-	6	18
19	69	1	1	6	1	6	3	-	-	1	-	-	-	-	-	1	-
20	75	1	1	57	6	2,057	14	237	6	10	-	6	223	39	-	5	25
X	442 (26)	10 (1)	5 (1)	67 (1)	6 (1)	54 (2)	17 (1)	39	6	9 (1)	-	5 (1)	42 (6)	10 (2)	-	7	1
Un	(644)	(24)	(12)	(414)	(37)	(2,246)	(67)	(860)	(37)	(56)	-	(34)	(711)	(115)	-	(31)	(1)
*Total*	3,698 (1,079)	110 (40)	74 (26)	2,240 (907)	233 (76)	15,403 (7,037)	432 (154)	4,439 (2,350)	247 (92)	318 (116)		214 (69)	5,516 (1,741)	792 (301)		212 (79)	267 (62)

Object count: Genetic maps

Chrm	FHH_x_ACI	SHRSP_x_BN
*Assembly: Reference* Mapped (Not placed)
1	74	250
2	49	226
3	31	162
4	34	161
5	30	119
6	33	93
7	49	85
8	23	101
9	38	63
10	44	113
11	20	49
12	12	50
13	47	92
14	24	72
15	39	76
16	24	50
17	23	76
18	17	58
19	22	37
20	22	25
X	29	63
*Total*	684	2,021

Object count: Physical maps

Chrm	MCW_RH
*Assembly: Reference* Mapped (Not placed)
1	2,937
2	1,950
3	1,629
4	1,686
5	1,810
6	1,276
7	1,581
8	1,611
9	894
10	1,184
11	704
12	782
13	830
14	680
15	720
16	849
17	898
18	771
19	625
20	591
X	319
*Total*	24,327

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